J. Biol. Chem., Vol. 266, Issue 9, 5521-5524, Mar, 1991
Highly restricted distributions of hydrophobic and charged amino acids in longitudinal quadrants of alpha-helices
RR Torgerson, RA Lew, VE Reyes, L Hardy and RE Humphreys
Department of Pharmacology, University of Massachusetts Medical Center, Worcester 01655.
Helix formation in folding proteins is stabilized by binding of recurrent
hydrophobic side chains in one longitudinal quadrant against the locally
most hydrophobic region of the protein. To test this hypothesis, we fitted
sequences of 247 alpha-helices of 55 proteins to the circular (infinite)
template (symbol; see text) to maximize the strip-of-helix hydrophobicity
index (the mean hydrophobicity of residues in (symbol; see text)
positions). These template-predicted configurations closely matched
crystallographic structures in 87% of four- or five-turn helices compared.
We determined the longitudinal quadrant distributions of amino acids in the
template-fitted, sheet projections of alpha-helices with respect to the
best longitudinal, hydrophobic strip on each helix and to the N and C
termini, interiors, and entire helices. Amino acids Leu, Ile, Val, and Phe
were concentrated in one longitudinal quadrant (p less than 0.001). Lys,
Arg, Asp, and Glu were not in the quadrant of Leu, Ile, Val, and Phe (p
less than 0.001). Significant quadrant distributions for other amino acids
and for termini of the helices were also found.
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
